Loading...

Current Issue

    28 May 2026, Volume 33 Issue 3 Previous Issue   

    Letters
    Reviews
    Research Papers
    For Selected: Toggle Thumbnails
    Letters
    Engineering Prime Editing System for Concurrent Gene Knockout and Point Mutation Induction (KAPSi) in Rice
    Liu Xiaoshuang, Ma Chong, Wang Dongmei, Xu Youshen, Qin Ruiying, Li Juan, Xu Rongfang, Wei Pengcheng
    2026, 33(3): 277-281.  DOI: 10.1016/j.rsci.2026.02.008
    Abstract ( )   HTML ( )   PDF (1179KB) ( )  
    Integrated Transcriptomic, Metabolomic, and Physio-Biochemical Analyses Reveal that NO and H2S Enhance Drought Tolerance in Upland Rice
    Mohammad Abass Ahanger, Li Yunfang, Biru Alemu Chali, Liu Guizhou, Lu Chengkai, Wan Jinpeng, Xu Peng
    2026, 33(3): 282-286.  DOI: 10.1016/j.rsci.2026.04.001
    Abstract ( )   HTML ( )   PDF (1012KB) ( )  
    Dual-Direction of DNA Methylome Reprogramming During Rice Domestication
    Yu Xiaoman, Cheng Xiang, Li Yilin, Yu Ruoqian, Liu Jiajia, Yang Lingwei, He Huiying, Wei Hua, Shang Lianguang, Wang Yuexing, Liu Xiangpei
    2026, 33(3): 287-291.  DOI: 10.1016/j.rsci.2026.02.005
    Abstract ( )   HTML ( )   PDF (1048KB) ( )  
    Evaluation of Leaf Spectra (150-1100 nm) in Tetraploid Rice and Their Spontaneously Reverted Diploid Counterparts
    Árpád Székely, Tímea Szalóki, Ildikó Kolozsvári, Aftab Jamal, Mihály Jancsó
    2026, 33(3): 292-296.  DOI: 10.1016/j.rsci.2026.04.002
    Abstract ( )   HTML ( )   PDF (758KB) ( )  
    Physicochemical Properties of Rice Hybrid Progeny from Parents with Divergent Resistant Starch Profiles
    Luo Mingrui, Jin Zhicheng, Liu Zhijie, Zhou Wangkai, Zheng Ruifeng, Huang Zehong, Shu Xiaoli, Wu Dianxing, An Zengxu
    2026, 33(3): 297-300.  DOI: 10.1016/j.rsci.2026.03.003
    Abstract ( )   HTML ( )   PDF (652KB) ( )  
    Identification of miRNA-mRNA Modules in Yuanjiang Common Wild Rice Conferring Resistance to Rice Blast
    Li Jinlu, Xiang Rong, Xiao Suqin, Zhang Yun, Chen Ling, Liu Li, Zhong Qiaofang, Yin Fuyou, Wang Bo, Xing Jiaxin, Jiang Cong, Zhang Dunyu, Zhu Yong, Zhao Shengli, Cheng Zaiquan
    2026, 33(3): 301-304.  DOI: 10.1016/j.rsci.2026.02.001
    Abstract ( )   HTML ( )   PDF (1074KB) ( )  
    Conversion of Double-Cropping Rice into Rice-Vegetable Rotation System Increases Net Economic Benefit with Lower Environmental Cost
    Li Fengbo, Wang Xiaoyu, Bao Ting, Mo Xiaorong, Zhou Mingzhuo, Xu Chunchun, Liu Yaobin, Feng Jinfei, Fang Fuping
    2026, 33(3): 305-308.  DOI: 10.1016/j.rsci.2026.03.001
    Abstract ( )   HTML ( )   PDF (482KB) ( )  
    Reviews
    Molecular and Functional Insights into Sugar Transporters in Rice
    Kieu Anh Thi Phan, Juho Lee, Cong Danh Nguyen, Sang-Kyu Lee
    2026, 33(3): 309-326.  DOI: 10.1016/j.rsci.2025.10.009
    Abstract ( )   HTML ( )   PDF (1823KB) ( )  

    Sugars are the main sources of energy and carbon for plants, making them crucial for various aspects of plant growth and development. Three prominent families of sugar transporters have been extensively researched: sucrose transporter, monosaccharide transporter, and sugars will eventually be exported transporter. The primary function of sugar transporters is to facilitate the movement of saccharide molecules, particularly sucrose and glucose, from cell to cell or from source tissues, such as leaves, to sink tissues like roots and developing seeds. Beyond mere transport, sugar transporters are integral to several biological and physiological processes in the plant. They are involved in phloem loading, which is critical for nutrient distribution throughout the plant, contribute to overall plant growth and development, and are essential in response to biotic (e.g., pathogen attack) and abiotic (e.g., drought or salinity) stresses. In this review, we provide a comprehensive summary and update on the functions of these sugar transporters, specifically in rice, and highlight the potential applications of gene editing technologies, which could be harnessed to enhance rice traits and improve yield.

    Advances in Rice Coleoptile Elongation: Implications for Direct-Seeded Rice Adaptation
    Fan Honghuan, Song Jian, Tang Liqun, Wang Junmin, Sheng Zhonghua, Jiao Guiai, Tang Shaoqing, Hu Shikai, Hu Peisong
    2026, 33(3): 327-339.  DOI: 10.1016/j.rsci.2026.02.004
    Abstract ( )   HTML ( )   PDF (1226KB) ( )  

    The rice coleoptile, a key protective structure during seed development, is crucial for safeguarding the plumule and facilitating seed germination. It plays a pivotal role in seedling emergence from soil, with its elongation characteristics being particularly important in direct-seeding systems. Coleoptile elongation is a complex biological process coordinately regulated by environmental factors, genetic background, plant hormones, and other signaling molecules, all of which interact to modulate elongation dynamics. This review systematically summarizes the mechanisms underlying coleoptile elongation, explores the regulatory roles of environmental and physiological factors, and synthesizes recent research progress on the identification of coleoptile-related QTLs, gene mining, and molecular regulatory mechanisms. Furthermore, we discuss the potential applications of coleoptile research in rice genetic improvement, aiming to provide a theoretical basis and novel insights for leveraging coleoptile traits in future breeding strategies.

    Advancing Rice Resilience to Heat Stress: Insights from CRISPR/Cas9 Genome Editing
    Zakirullah Khan, Rahmatullah Jan, Saleem Asif, Hayati Aulia Maharani, Muhammad Farooq, Kyung-Min Kim
    2026, 33(3): 340-350.  DOI: 10.1016/j.rsci.2026.02.003
    Abstract ( )   HTML ( )   PDF (1135KB) ( )  

    Heat stress during reproductive stages remains one of the most critical constraints on rice yield and grain quality, yet progress in developing heat-resilient cultivars is slowed by the complex, polygenic nature of thermotolerance and lengthy breeding cycles. Despite incremental gains through conventional breeding, high temperatures above 35 ºC continue to cause severe spikelet sterility, yield losses, and quality deterioration. The emergence of CRISPR/Cas genome-editing offers a precise and efficient platform to dissect heat-stress mechanisms, and accelerate the development of heat-tolerant rice. CRISPR/Cas9 studies have validated and edited key genes involved in calcium signaling, hormone pathways, reproductive processes, photosynthesis, reactive oxygen species homeostasis, and transcriptional regulation, such as OsCNGC14/16, OsNCED1, OsSPL7, and OsHSP60-3b. Beyond stress resilience, genome editing has improved major yield components, including grain size, panicle architecture, and spikelet number, through targets such as GS3, GW3, Gn1a, and OsSPL16, achieving 28%-40% increases in grain weight and 15%-25% improvements in panicle traits, alongside enhanced grain quality attributes. Remaining challenges, including off-target effects, genotype dependence, limited field validation, and regulatory constraints, are being addressed through high-fidelity Cas variants, optimized sgRNA design, DNA-free editing, and integration with genomic selection and speed breeding. This review synthesizes advances in heat-stress biology and CRISPR/Cas applications in rice, and highlights future opportunities in base and prime editing, transcriptional reprogramming, multiplex genome engineering, and field deployment.

    Research Papers
    Enigma of Prolonged Submergence Tolerance in Rice: Rediscovering Critical Factors Beyond SUB1A
    Koushik Chakraborty, Subhankar Mondal, Biswaranjan Das, Priyanka Jena, Sagar Banerjee, Mridul Chakraborti, Krishnendu Chattopadhyay, Ramani Kumar Sarkar
    2026, 33(3): 351-366.  DOI: 10.1016/j.rsci.2026.02.009
    Abstract ( )   HTML ( )   PDF (2275KB) ( )  

    The discovery and subsequent introgression of SUB1A-1 gene into rice produces remarkable success in tolerating complete submergence for about two weeks. However, the tolerance of Sub1-introgressed cultivar Swarna Sub1 is still inferior to that of FR13A, the donor of the gene. To investigate this discrepancy, we examined the submergence tolerance potential of FR13A and several superior landraces that show significantly better tolerance than Swarna Sub1 under prolonged submergence. We found that several landraces (AC42088, AC42087, and AC1303) and FR13A carried functional alleles of both SUB1 and SNORKEL genes, along with a dominant allele of SD1. Genotypes carrying the SD1 allele exhibited greater initial plant height, and the combined presence of both SUB1 and SNORKEL genes might confer better survivability by allowing moderate shoot elongation under prolonged submergence, particularly beyond two weeks. Interestingly, OsSUB1A-1 expression was not suppressed despite high expression of SNORKEL genes in several superior landraces and FR13A. These genotypes also had relatively thicker leaf gas films and delayed depletion of those films under water. Higher epicuticular wax concentration in these genotypes contributed to prolonged persistence of the gas film and improved maintenance of chlorophyll in inundated leaf tissues. Scanning electron microscopy revealed a thick layer of deposition on the leaf surfaces of these landraces and FR13A. Higher transcript abundance of wax biosynthesis genes and a strong, positive, significant correlation between these transcripts and leaf wax concentration suggested the presence of very long-chain fatty acids that may delay loss of leaf hydrophobicity in these landraces. Overall, this study suggests that SUB1A-mediated quiescence, supplemented by moderate elongation via SNORKEL genes, could be beneficial for survival under prolonged submergence beyond two weeks.

    Genetic Variation and Population Structure of Asian Cultivated Rice
    Li Wei, Zhang Mengchen, Chen Xiaoyang, Li Yan, Xu Qun, Wang Shan, Feng Yue, Wei Xinghua, Yang Yaolong
    2026, 33(3): 367-380.  DOI: 10.1016/j.rsci.2026.02.010
    Abstract ( )   HTML ( )   PDF (1770KB) ( )  

    Rice germplasms serve as repositories of genetic variation. Population structure analysis is crucial for the effective utilization of rice germplasm and provides an evolutionary framework for future biological research. In this study, we constructed a genetic variation map using a large population of 20 056 rice accessions. A total of 34 426 306 variants were identified, including 29 251 099 biallelic and 5 175 207 multiallelic variants. Population structure analysis of a subset of 5 668 accessions classified Asian cultivated rice into eight distinct groups: temperate japonica 1 (TEJ1), temperate japonica 2 (TEJ2), tropical japonica (TRJ), aromatic (ARO), aus (AUS), indica 1 (IND1), indica 2 (IND2), indica 3 (IND3). Comparative analysis revealed that japonica accessions from China were predominantly composed of TEJ1 and TEJ2, while indica varieties were mainly from IND1. In contrast, introduced japonica accessions were primarily TEJ1 and TRJ, with IND2 representing the major indica group. Foreign accessions represented all eight groups, whereas Chinese accessions lacked the ARO, AUS, and IND3 groups. Genetic diversity analysis revealed that IND3 and TEJ1 exhibited the highest and lowest nucleotide diversity, respectively. Geographically, TRJ was largely distributed in the Americas, ARO was concentrated in the Middle East, and notably, TEJ2 was identified as a group specific to China. Furthermore, we identified 52 regions with significant genetic differentiation. Two of these regions, harboring the cold-tolerant genes bZIP73 and COLD1, were selected for further analysis. Nucleotide diversity and haplotype network analyses indicated that both genes may have undergone positive selection and contribute to indica-japonica differentiation. Haplotype analysis also uncovered novel alleles, including a new mutation in COLD1 that may represent a favorable variant for enhancing cold tolerance in japonica accessions. Our study demonstrates that large-scale population analysis of genetic variation is a powerful method for dissecting population structure, elucidating the mechanisms of genetic differentiation, and identifying novel functional alleles.

    A Low-Cost RGB-Based Image Processing Method for High-Throughput Assessment of Rice Grain Chalkiness
    Jardel da Silva Souza, Sandra Helena Uneda-Trevisoli, Felipe Dalla Lana, Roberto Fritsche-Neto
    2026, 33(3): 381-391.  DOI: 10.1016/j.rsci.2025.12.003
    Abstract ( )   HTML ( )   PDF (1499KB) ( )  

    Although numerous rice genotypes have been developed worldwide, post-harvest evaluation of chalkiness, a key grain trait, remains a significant challenge in breeding programs. Conventional phenotyping methods rely on manual grain separation and analysis, which limit the speed and performance of decision-making. This study aimed to assess the efficiency of a low-cost, image-based phenotyping method for characterizing rice grain chalkiness and morphological traits (grain length and width) in comparison with traditional evaluation methods. Grains from 270 rice samples were imaged using a hyperspectral camera (visible to near-infrared, 400-1 000 nm) and a Nikon digital single-lens reflex (DSLR) camera. Only RGB information was used for analysis, including RGB channels extracted from hyperspectral imagery to simulate low-cost setups. Python scripts were used to segment grains, estimate morphological parameters, and calculate chalkiness degree. Results from both imaging systems were compared with reference data obtained from the SeedCount platform. Strong correlations with SeedCount reference data were observed for chalkiness degree, reaching 93% when using hyperspectral-derived RGB data and 76% when using DSLR-acquired RGB images. Binary classification metrics showed high discriminative performance, with area under the curve (AUC) values above 0.90 for most traits. The proposed method enabled image acquisition and processing in approximately 21 s per sample, compared to 1.5 min required by the conventional platform. The findings demonstrate the feasibility of a rapid and low-cost image-based phenotyping strategy to support rice breeding programs, particularly for chalkiness quantification and grain morphology assessment. The complete image-processing pipeline is provided as supplementary material, reinforcing the transparency and reproducibility of the method.

    Global Patterns of Stage-Specific Alternative Polyadenylation in Rice Tillering Revealed by Nanopore Long Read Sequencing and Proteomics
    Li Xinyi, Huang Junying, Zhou Dahu, Cai Yicong, Chen Xiaorong, Hu Lifang, Ouyang Linjuan, Fu Junru, Li Qingshun, He Haohua, Fu Haihui
    2026, 33(3): 392-410.  DOI: 10.1016/j.rsci.2026.03.002
    Abstract ( )   HTML ( )   PDF (2214KB) ( )  

    Tiller number is a crucial agronomic trait that directly influences the grain yield per unit area of rice. Alternative polyadenylation (APA), an essential post-transcriptional regulatory mechanism, plays a significant role in rice growth and development by generating transcripts with varying 3ʹ untranslated region (3ʹUTR) lengths. However, the specific role of APA in rice tillering remains poorly understood. We employed nanopore cDNA sequencing and tandem mass tag proteomics to analyze tiller axillary buds at different developmental stages in rice. Our findings revealed that genes at the early stages of tillering (effective tillering) tend to utilize longer transcripts, whereas those at the later stages (ineffective tillering) favor shorter transcripts. APA-related genes at both the effective and ineffective tillering stages are enriched in known rice tillering-associated pathways, such as the terpenoid backbone biosynthesis pathway and the carotenoid biosynthesis pathway. Additionally, APA-related genes at the ineffective tillering stage are further enriched in pathways such as leaf and organ senescence. The results demonstrate that APA-mediated gene length variation regulates rice tillering in a spatiotemporally specific pattern, and APA further impacts the protein abundance of genes involved in tillering. Genes that utilize the distal AAUAAA signal and produce longer transcripts exhibit stronger expression than those using the proximal signal, while genes using the proximal AAUAAA signal and generating shorter transcripts show stronger expression than those using the distal signal. This study clarifies the regulatory patterns of APA in rice tillering, laying a molecular foundation for the potential breeding of rice with ideal plant architecture.